Methods, compositions, and kits for blocking a capture probe on a spatial array

ABSTRACT

Provided are methods for determining a location of a target nucleic acid in a biological sample including: disposing the biological sample onto an array including a plurality of capture probes, where a first capture probe includes a first spatial barcode and a capture domain and a second capture probe includes a second spatial barcode and the capture domain. The second capture probe is not covered by the biological sample on the array and is contacted with a solution comprising TdT and one or more dideoxynucleotides, such that a dideoxynucleotide is incorporated into the second capture domain. Target nucleic acids are captured by the first capture probe, and the sequence of the first spatial barcode or a complement thereof and all or a portion of a sequence of the target nucleic acid, or a complement thereof, are used to determine the location of the target nucleic acid in the biological sample.

CROSS-REFERENCE TO RELATED APPLICATIONS

Pursuant to 35 U.S.C. § 119(e), this application is a continuation of International Application PCT/US2022/042320, with an international filing date of Sep. 1, 2022, which claims the benefit of U.S. Provisional Patent Application No. 63/239,612, filed on Sep. 1, 2021. The content of that patent application is incorporated herein by reference in its entirety.

BACKGROUND

Cells within a tissue have differences in cell morphology and/or function due to varied analyte levels (e.g., gene and/or protein expression) within the different cells. The specific position of a cell within a tissue (e.g., the cell's position relative to neighboring cells or the cell's position relative to the tissue microenvironment) can affect, e.g., the cell's morphology, differentiation, fate, viability, proliferation, behavior, signaling, and cross-talk with other cells in the tissue.

Spatial heterogeneity has been previously studied using techniques that typically provide data for a handful of analytes in the context of intact tissue or a portion of a tissue (e.g., tissue section), or provide significant analyte data from individual, single cells, but fails to provide information regarding the position of the single cells from the originating biological sample (e.g., tissue).

Some techniques for studying spatial heterogeneity of a biological sample can cause analytes (e.g., nucleic acids) from the biological sample to diffuse to areas adjacent to the biological sample and be captured in such areas adjacent to the biological sample, or not as proximate to the original location of the analyte in the biological sample as is desired. The capturing of analytes on areas adjacent to the biological sample on the array (e.g., areas that are not covered by the biological sample) can lead to wasted resources, such as for example, unnecessary costs attributed to sequencing (e.g., next generation sequencing) as well as decreased resolution and accuracy of the spatial information from the biological sample. Thus, methods to decrease the incidence of captured analytes on areas of the array adjacent to the biological sample (e.g., by decreasing capture of analytes on areas not covered by the biological sample), can improve efficiency, resource conservation, and resolution of results.

SUMMARY

This application generally features methods to block capture probes on an array (e.g., a spatial array) that are not under or covered by a biological sample placed on the array. Methods described herein include methods to block capture probes on a spatial array using terminal deoxynucleotidyl transferase (TdT) and one or more dideoxynucleotides. The methods described herein can provide an improvement in resource conservation (e.g., reduced library for sequencing) and a reduction and/or elimination of binding (e.g., of analytes to unintended portions of the spatial array (e.g., portions of the array not under or covered by the biological sample) during performance of any of the methods described herein (e.g., determining a location of a target analyte in a biological sample).

Provided herein are methods for determining a location of a target nucleic acid in a biological sample, the method including: (a) disposing a biological sample onto an array at a first rea, where the array includes a plurality of capture probes, where: a first capture probe of the plurality of capture probes includes a spatial barcode and a capture domain, where the first capture probe is included in the first area of the array; and a second area of the array includes a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array; (b) contacting the second area of the array with a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are incorporated into the capture domain of the second capture probe; (c) removing residual solution from the second area of the array; (d) permeabilizing the biological sample, such that the capture domain of the first capture probe hybridizes to the target nucleic acid from the biological sample; and (e) determining (i) a sequence corresponding to the spatial barcode of the first capture probe, or a complement thereof, and (ii) all or a portion of a sequence corresponding to the target nucleic acid, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.

In some embodiments, the removing step includes the use of a wash buffer including one or more of: a solvent, an acid, a base, and a buffer. In some embodiments, the wash buffer includes phosphate buffered saline or saline sodium citrate.

In some embodiments, the determining in step (e) includes extending a 3′ end of the capture probe of the first area of the array using the target nucleic acid as a template. In some embodiments, the determining in step (e) includes sequencing (i) the spatial barcode of the capture probe of the first area of the array, or a complement thereof, and (ii) all or a portion of the target nucleic acid, or a complement thereof. In some embodiments, the sequencing is high throughput sequencing.

In some embodiments, the permeabilizing includes use of a permeabilization agent selected from an organic solvent, a detergent, an enzyme, and combinations thereof. In some embodiments, the permeabilization agent is selected from the group consisting of: an endopeptidase, a protease, sodium dodecyl sulfate, polyethylene glycol tert-octylphenyl ether, polysorbate 80, polysorbate 20, N-lauroylsarcosine sodium salt solution, saponin, Triton X-100™, and Tween-20™. In some embodiments, the endopeptidase is pepsin or proteinase K.

Also provided herein are methods of blocking capture probes not covered by a biological sample, the method including: (a) disposing a biological sample onto an array at a first area, where the array includes a plurality of capture probes, where: a first capture probe of the plurality of capture probes includes a spatial barcode and a capture domain, where the first capture probe is included in the first area of the array; and a second area of the array includes a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array; and (b) contacting the second area of the array with a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are incorporated into the capture domain of the second capture probe in the second area.

In some embodiments, the method includes step (c) permeabilizing the biological sample, such that the capture domain of the first capture probe hybridizes to the target nucleic acid from the biological sample. In some embodiments, step (c) includes contacting the biological sample with a permeabilization agent, where the permeabilization agent is selected from an organic solvent, a detergent, an enzyme, and combinations thereof. In some embodiments, the permeabilization agent is selected from the group consisting of: an endopeptidase, a protease, sodium dodecyl sulfate, polyethylene glycol tert-octylphenyl ether, polysorbate 80, polysorbate 20, N-lauroylsarcosine sodium salt solution, saponin, Triton X-100™, and Tween-20™. In some embodiments, the endopeptidase is pepsin or proteinase K.

In some embodiments, the method includes removing residual solution from the second area of the array prior to permeabilization. In some embodiments, the removing step includes the use of a wash buffer including one or more of: a solvent, an acid, a base, and a buffer. In some embodiments, the wash buffer includes phosphate buffered saline or saline sodium citrate.

In some embodiments, the biological sample is fixed and/or stained prior to step (a). In some embodiments, the method includes, between steps (a) and (b), fixing and/or staining the biological sample.

In some embodiments, the step of fixing the biological sample includes the use of a fixative selected from the group consisting of: ethanol, methanol, acetone, formaldehyde, paraformaldehyde-Triton, glutaraldehyde, and combinations thereof.

In some embodiments, the step of staining the biological sample includes the use of eosin and/or hematoxylin.

In some embodiments, the step of staining the biological sample includes the use of a detectable label selected from the group consisting of a radioisotope, a fluorophore, a chemiluminescent compound, a bioluminescent compound, and a combination thereof.

Also provided herein are methods for determining a location of a target nucleic acid in a biological sample, the method including: (a) disposing a biological sample onto an array at a first area, where the array includes a plurality of capture probes, where: a first capture probe of the plurality of capture probes includes a spatial barcode and a capture domain, where the first capture probe is included in the first area of the array; and a second area of the array includes a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array, where the capture domain of the first capture probe hybridizes to a ligation product; (b) extending the ligation product toward the 5′ end of the first capture probe using the first capture probe as a template; (c) contacting the second area of the array with a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are incorporated into the capture domain of the second capture probe; (d) removing residual solution from the second area of the array; and (e) determining (i) a sequence corresponding to the spatial barcode of the first capture probe, or a complement thereof, and (ii) all or a portion of a sequence corresponding to the ligation product, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.

In some embodiments, the removing step includes the use of a wash buffer including one or more of: a solvent, an acid, a base, and a buffer. In some embodiments, the wash buffer includes phosphate buffered saline or saline sodium citrate.

In some embodiments, the extending in step (b) includes extending a 3′ end of the first capture probe using the ligation product as a template.

In some embodiments, the determining in step (e) includes sequencing (i) the spatial barcode of the first capture probe, or a complement thereof, and (ii) all or a portion of the ligation product, or a complement thereof. In some embodiments, the sequencing is high throughput sequencing.

Also provided herein are methods of blocking capture probes to decrease barcode exchange and/or decrease the use of capture probes as extension templates, the method including: (a) disposing a biological sample onto an array at a first area, where the array includes a plurality of capture probes, where: a first capture probe of the plurality of capture probes includes a spatial barcode and a capture domain, where the first capture probe is included in the first area of the array; and a second area of the array includes a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array, where the capture domain of the first capture probe hybridizes to a ligation product; (b) extending the ligation product toward the 5′ end of the first capture probe using the first capture probe as a template; and (c) contacting the second area of the array with a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are incorporated into the capture domain of the second capture probe.

In some embodiments, the method includes removing residual solution from the second area of the array. In some embodiments, the removing step includes the use of a wash buffer including one or more of: a solvent, an acid, a base, and a buffer. In some embodiments, the wash buffer includes phosphate buffered saline or saline sodium citrate.

In some embodiments, the biological sample is fixed and/or stained prior to step (a). In some embodiments, the method includes, between steps (a) and (b), fixing and/or staining the biological sample.

In some embodiments, the step of fixing the biological sample includes the use of a fixative selected from the group consisting of ethanol, methanol, acetone, formaldehyde, paraformaldehyde-Triton, glutaraldehyde, and combinations thereof. In some embodiments, the step of staining the biological sample includes the use of eosin and/or hematoxylin.

In some embodiments, the step of staining the biological sample includes the use of a detectable label selected from the group consisting of a radioisotope, a fluorophore, a chemiluminescent compound, a bioluminescent compound, and a combination thereof.

In some embodiments, the ligation product is generated by hybridizing a first probe and a second probe to the target nucleic acid, where the first probe and the second probe are ligated to form the ligation product. In some embodiments, the first probe or the second probe includes an analyte capture sequence that hybridizes to the capture domain of the first capture probe.

In some embodiments, the one or more dideoxynucleotides is ddATP or ddTTP. In some embodiments, the solution includes about 0.5 mM of the one or more dideoxynucleotides to about 25 mM of the one or more dideoxynucleotides. In some embodiments, the solution includes about 0.5 mM of the one or more dideoxynucleotides to about 1.5 mM of the one or more dideoxynucleotides. In some embodiments, the solution includes about 1 mM of the one or more dideoxynucleotides.

In some embodiments, the solution includes CoCl₂. In some embodiments, the solution includes about 0.1 mM CoCl₂ to about 2 mM CoCl₂. In some embodiments, the solution includes about 0.25 mM CoCl₂.

In some embodiments, the solution includes a buffer.

In some embodiments, the contacting step is performed for about 5 minutes to about 90 minutes. In some embodiments, the contacting step is performed for about 60 minutes. In some embodiments, the contacting step is performed at a temperature of about 25° C. to about 45° C. In some embodiments, the contacting step is performed at a temperature of about 37° C.

Also provided herein are kits including: (a) a solution including terminal deoxynucleotidyl transferase; (b) one or more dideoxynucleotides; (c) a substrate including a plurality of capture probes, where a capture probe of the plurality of capture probes include a spatial barcode and a capture domain; and (d) instructions for performing any of the methods described herein.

In some embodiments, the kit includes a fixative selected from the group consisting of ethanol, methanol, acetone, formaldehyde, paraformaldehyde-Triton, glutaraldehyde, and combinations thereof.

In some embodiments, the one or more dideoxynucleotides are ddATP and/or ddTTP. In some embodiments, the solution includes about 0.5 mM of the one or more dideoxynucleotides to about 25 mM of the one or more dideoxynucleotides. In some embodiments, the solution includes about 0.5 mM of the one or more dideoxynucleotides to about 1.5 mM of the one or more dideoxynucleotides. In some embodiments, the solution includes about 1 mM of the one or more dideoxynucleotides.

In some embodiments, the solution includes CoCl₂. In some embodiments, the solution includes about 0.1 mM CoCl₂ to about 2 mM CoCl₂. In some embodiments, the solution includes about 0.25 mM CoCl₂.

In some embodiments, the solution includes a buffer. In some embodiments, the kit includes a wash buffer including one or more of: a solvent, an acid, a base, and a buffer. In some embodiments, the wash buffer includes phosphate buffered saline. In some embodiments, the wash buffer includes saline sodium citrate.

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, patent application, or item of information was specifically and individually indicated to be incorporated by reference. To the extent publications, patents, patent applications, and items of information incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and/or take precedence over any such contradictory material.

Where values are described in terms of ranges, it should be understood that the description includes the disclosure of all possible sub-ranges within such ranges, as well as specific numerical values that fall within such ranges irrespective of whether a specific numerical value or specific sub-range is expressly stated.

The term “each,” when used in reference to a collection of items, is intended to identify an individual item in the collection but does not necessarily refer to every item in the collection, unless expressly stated otherwise, or unless the context of the usage clearly indicates otherwise.

Various embodiments of the features of this disclosure are described herein. However, it should be understood that such embodiments are provided merely by way of example, and numerous variations, changes, and substitutions can occur to those skilled in the art without departing from the scope of this disclosure. It should also be understood that various alternatives to the specific embodiments described herein are also within the scope of this disclosure.

DESCRIPTION OF DRAWINGS

The following drawings illustrate certain embodiments of the features and advantages of this disclosure. These embodiments are not intended to limit the scope of the appended claims in any manner. Like reference symbols in the drawings indicate like elements.

FIG. 1 is a schematic diagram showing an example of a barcoded capture probe, as described herein.

FIG. 2 shows an example workflow diagram for a method for blocking the capture probes adjacent to a biological sample on a spatial array and determining a location of a target nucleic acid in a biological sample.

FIG. 3 shows an exemplary workflow diagram for mitigating the possibility of capture probes acting as primers and determining a location of a target nucleic acid in a biological sample.

DETAILED DESCRIPTION

The result of capturing nucleic acid analytes, or proxies thereof, on areas adjacent to a biological sample on an array (e.g., areas that are not under or covered with the biological sample) can lead to wasted resources, such as unnecessary costs attributed to sequencing (e.g., next generation sequencing) and can compromise spatial resolution. Blocking one or more capture domains of capture probes on spatial arrays (or portions thereof) can increase efficiency and/or decrease binding of analytes on arrays (or portions thereof). In some cases, one or more capture probes (e.g., capture domain of capture probes) can be blocked using terminal deoxynucleotidyl transferase and one or more dideoxynucleotides. Provided herein are methods, compositions, and kits for carrying out these methods.

Methods for reducing spatial interactions on a spatial array on areas not under or covered by a biological sample are described herein. The methods described herein can improve the resolution of spatial array results by reducing binding of nucleic acid analytes or proxies thereof on areas of the array that do not correlate with the original location of the biological sample on the array. In some cases, nucleic acid analytes from a biological sample can diffuse (e.g., laterally) to areas of the array that are not covered by the biological sample, which can result in analytes binding to the capture domain(s) of one or more capture probes not covered by the biological sample. Analyte capture on areas adjacent or proximal to the biological sample increase background results and decrease resolution. Blocking the capture domain of capture probes that are adjacent or proximal to the biological sample can decrease the unwanted binding and increase the resolution of target capture. Thus, the present disclosure features methods, compositions, and kits that can reduce the capture of nucleic acid analytes on areas adjacent to or not covered by the biological sample by preventing binding of analytes to those capture probes adjacent or proximal to the biological sample (e.g., by blocking the capture domain of capture probes).

The methods described herein can also conserve resources. For example, in some cases, the analysis of data obtained from nucleic analytes captured on an array (e.g., a spatial array) can include sequencing. Unwanted binding of nucleic acid analytes to the capture domain of one or more capture probes can result in sequencing of nucleic acid analytes captured in areas not covered by the biological sample. Unwanted nucleic acid analyte capture (or proxies thereof) can also cause downstream sequencing inefficiencies, for example, a decrease in the amount of nucleic acid analyte sequencing due to sequencing of unwanted captured analytes is inefficient and reagent costly and can result in a decrease in spatial resolution. The present disclosure provides solutions for improving and/or preventing unwanted nucleic acid analyte (or proxies thereof capture on an array.

The methods described herein include blocking the capture domain of one or more capture probes located in areas not under or covered by a biological sample on an array using terminal deoxynucleotidyl transferase and nucleotide triphosphates. Terminal deoxynucleotidyl transferase can transfer nucleotide triphosphates to the 3′ hydroxyl end of oligonucleotides. For example, incorporating one or more dideoxynucleotides into the 3′ end of a capture probe with terminal deoxynucleotidyl transferase can prevent ligation or polymerase extensions, including reverse transcription.

In some embodiments, terminal deoxynucleotidyl transferase and one or more dideoxynucleotides are applied to the portions of the array that are not covered by a biological sample prior to permeabilization of the biological sample. In this way, the extension of capture probes that are not under or covered by the biological sample is prevented. This can reduce wasted resources by prevention of reads from capture probes in areas adjacent to the biological sample, and also reduce mislocalized analytes that may appear in voids or spaces in the biological sample (e.g., airways in biological samples such as lung tissue). In other embodiments, applying terminal deoxynucleotidyl transferase and one or more dideoxynucleotides after second strand synthesis, but prior to amplification, can reduce or eliminate barcode exchange that results from capture probes acting as extension templates (e.g., primers).

As used herein “barcode exchange” or a “barcode exchange reaction” refers to excess or extra barcoded molecules (e.g., capture probes that include a spatial barcode) that function as extension templates. As used herein capture probes not covered by the biological sample can function as an extension template and introduce a different barcode (e.g., a spatial barcode) than the parent template molecule during amplification such as second strand synthesis. In some examples, barcode exchange can occur during preparation of sequencing libraries. Barcode exchange and barcode exchange reactions are further described in WO 2020/028882, which is incorporated herein by reference in its entirety.

Spatial analysis methodologies and compositions described herein can provide a vast amount of analyte and/or expression data for a variety of analytes within a biological sample at high spatial resolution, while retaining native spatial context. Spatial analysis methods and compositions can include, e.g., the use of a capture probe including a spatial barcode (e.g., a nucleic acid sequence that provides information as to the location or position of an analyte within a cell or a tissue sample (e.g., mammalian cell or a mammalian tissue sample) and a capture domain that is capable of binding to an analyte (e.g., a protein and/or a nucleic acid) produced by and/or present in a cell. Spatial analysis methods and compositions can also include the use of a capture probe having a capture domain that captures an intermediate agent for indirect detection of an analyte. For example, the intermediate agent can include a nucleic acid sequence (e.g., a barcode) associated with the intermediate agent. Detection of the intermediate agent is therefore indicative of the analyte in the cell or tissue sample.

Non-limiting aspects of spatial analysis methodologies and compositions are described in U.S. Pat. Nos. 10,774,374, 10,724,078, 10,480,022, 10,059,990, 10,041,949, 10,002,316, 9,879,313, 9,783,841, 9,727,810, 9,593,365, 8,951,726, 8,604,182, 7,709,198, U.S. Patent Application Publication Nos. 2020/239946, 2020/080136, 2020/0277663, 2020/024641, 2019/330617, 2019/264268, 2020/256867, 2020/224244, 2019/194709, 2019/161796, 2019/085383, 2019/055594, 2018/216161, 2018/051322, 2018/0245142, 2017/241911, 2017/089811, 2017/067096, 2017/029875, 2017/0016053, 2016/108458, 2015/000854, 2013/171621, WO 2018/091676, WO 2020/176788, Rodrigues et al., Science 363(6434):1463-1467, 2019; Lee et al., Nat. Protoc. 10(3):442-458, 2015; Trejo et al., PLoS ONE 14(2):e0212031, 2019; Chen et al., Science 348(6233):aaa6090, 2015; Gao et al., BMC Biol. 15:50, 2017; and Gupta et al., Nature Biotechnol. 36:1197-1202, 2018; the Visium Spatial Gene Expression Reagent Kits User Guide (e.g., Rev C, dated June 2020), and/or the Visium Spatial Tissue Optimization Reagent Kits User Guide (e.g., Rev C, dated July 2020), both of which are available at the 10× Genomics Support Documentation website, and can be used herein in any combination. Further non-limiting aspects of spatial analysis methodologies and compositions are described herein.

Some general terminology that may be used in this disclosure can be found in Section (I)(b) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663. Typically, a “barcode” is a label, or identifier, that conveys or is capable of conveying information (e.g., information about an analyte in a sample, a bead, and/or a capture probe). A barcode can be part of an analyte, or independent of an analyte. A barcode can be attached to an analyte. A particular barcode can be unique relative to other barcodes. For the purpose of this disclosure, an “analyte” can include any biological substance, structure, moiety, or component to be analyzed. The term “target” can similarly refer to an analyte of interest.

Analytes can be broadly classified into one of two groups: nucleic acid analytes, and non-nucleic acid analytes. Examples of non-nucleic acid analytes include, but are not limited to, lipids, carbohydrates, peptides, proteins, glycoproteins (N-linked or O-linked), lipoproteins, phosphoproteins, specific phosphorylated or acetylated variants of proteins, amidation variants of proteins, hydroxylation variants of proteins, methylation variants of proteins, ubiquitylation variants of proteins, sulfation variants of proteins, viral proteins (e.g., viral capsid, viral envelope, viral coat, viral accessory, viral glycoproteins, viral spike, etc.), extracellular and intracellular proteins, antibodies, and antigen binding fragments. In some embodiments, the analyte(s) can be localized to subcellular location(s), including, for example, organelles, e.g., mitochondria, Golgi apparatus, endoplasmic reticulum, chloroplasts, endocytic vesicles, exocytic vesicles, vacuoles, lysosomes, etc. In some embodiments, analyte(s) can be peptides or proteins, including without limitation antibodies and enzymes. Additional examples of analytes can be found in Section (I)(c) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663. In some embodiments, an analyte can be detected indirectly, such as through detection of an intermediate agent, for example, a ligation product or an analyte capture agent (e.g., an oligonucleotide-conjugated antibody), such as those described herein.

A “biological sample” is typically obtained from the subject for analysis using any of a variety of techniques including, but not limited to, biopsy, surgery, and laser capture microscopy (LCM), and generally includes cells from the subject. In some embodiments, a biological sample can be a tissue section. In some embodiments, a biological sample can be a fixed and/or stained biological sample (e.g., a fixed and/or stained tissue section). Non-limiting examples of stains include histological stains (e.g., hematoxylin and/or eosin) and immunological stains (e.g., fluorescent stains). In some embodiments, a biological sample (e.g., a fixed and/or stained biological sample) can be imaged. Biological samples are also described in Section (I)(d) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663.

In some embodiments, a biological sample is permeabilized with one or more permeabilization reagents. For example, permeabilization of a biological sample can facilitate analyte capture. Exemplary permeabilization agents and conditions are described in Section (I)(d)(ii)(13) or the Exemplary Embodiments Section of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663.

Array-based spatial analysis methods involve the transfer of one or more analytes from a biological sample to an array of features on a substrate, where each feature is associated with a unique spatial location on the array. Subsequent analysis of the transferred analytes includes determining the identity of the analytes and the spatial location of the analytes within the biological sample. The spatial location of an analyte within the biological sample is determined based on the feature to which the analyte is bound (e.g., directly or indirectly) on the array, and the feature's relative spatial location within the array.

A “capture probe” refers to any molecule capable of capturing (directly or indirectly) and/or labelling an analyte (e.g., an analyte of interest) in a biological sample. In some embodiments, the capture probe is a nucleic acid or a polypeptide. In some embodiments, the capture probe includes a barcode (e.g., a spatial barcode and/or a unique molecular identifier (UMI)) and a capture domain). In some embodiments, a capture probe can include a cleavage domain and/or a functional domain (e.g., a primer-binding site, such as for next-generation sequencing (NGS)). See, e.g., Section (II)(b) (e.g., subsections (i)-(vi)) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663. Generation of capture probes can be achieved by any appropriate method, including those described in Section (II)(d)(ii) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663.

In some embodiments, more than one analyte type (e.g., nucleic acids and proteins) from a biological sample can be detected (e.g., simultaneously or sequentially) using any appropriate multiplexing technique, such as those described in Section (IV) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663.

In some embodiments, detection of one or more analytes (e.g., protein analytes) can be performed using one or more analyte capture agents. As used herein, an “analyte capture agent” refers to an agent that interacts with an analyte (e.g., an analyte in a biological sample) and with a capture probe (e.g., a capture probe attached to a substrate or a feature) to identify the analyte. In some embodiments, the analyte capture agent includes: (i) an analyte binding moiety (e.g., that binds to an analyte), for example, an antibody or antigen-binding fragment thereof; (ii) analyte binding moiety barcode; and (iii) an analyte capture sequence. As used herein, the term “analyte binding moiety barcode” refers to a barcode that is associated with or otherwise identifies the analyte binding moiety. As used herein, the term “analyte capture sequence” refers to a region or moiety configured to hybridize to, bind to, couple to, or otherwise interact with a capture domain of a capture probe. In some cases, an analyte binding moiety barcode (or portion thereof) may be able to be removed (e.g., cleaved) from the analyte capture agent. Additional description of analyte capture agents can be found in Section (II)(b)(ix) of WO 2020/176788 and/or Section (II)(b)(viii) U.S. Patent Application Publication No. 2020/0277663.

There are at least two methods to associate a spatial barcode with one or more neighboring cells, such that the spatial barcode identifies the one or more cells, and/or contents of the one or more cells, as associated with a particular spatial location. One method is to promote analytes or analyte proxies (e.g., intermediate agents) out of a cell and towards a spatially-barcoded array (e.g., including spatially-barcoded capture probes). Another method is to cleave spatially-barcoded capture probes from an array and promote the spatially-barcoded capture probes towards and/or into or onto the biological sample.

In some cases, capture probes may be configured to prime, replicate, and consequently yield optionally barcoded extension products from a template (e.g., a DNA or RNA template, such as an analyte or an intermediate agent (e.g., a ligation product or an analyte capture agent), or a portion thereof), or derivatives thereof (see, e.g., Section (II)(b)(vii) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663 regarding extended capture probes). In some cases, capture probes may be configured to form ligation products with a template (e.g., a DNA or RNA template, such as an analyte or an intermediate agent, or portion thereof), thereby creating ligations products that serve as proxies for a template.

As used herein, an “extended capture probe” refers to a capture probe having additional nucleotides incorporated (e.g., added) to the terminus (e.g., 3′ or 5′ end) of the capture probe thereby extending the overall length of the capture probe. For example, an “extended 3′ end” indicates additional incorporated nucleotides were added to the most 3′ nucleotide of the capture probe to extend the length of the capture probe, for example, by polymerization reactions used to extend nucleic acid molecules including templated polymerization catalyzed by a polymerase (e.g., a DNA polymerase or a reverse transcriptase). In some embodiments, extending the capture probe includes adding to a 3′ end of a capture probe a nucleic acid sequence that is complementary to a nucleic acid sequence of an analyte or intermediate agent specifically bound to the capture domain of the capture probe. In some embodiments, the capture probe is extended using reverse transcription. In some embodiments, the capture probe is extended using one or more DNA polymerases. The extended capture probes include the sequence of the capture probe and the sequence of the spatial barcode of the capture probe.

In some embodiments, extended capture probes are amplified (e.g., in bulk solution or on the array) to yield quantities that are sufficient for downstream analysis, e.g., via DNA sequencing. In some embodiments, extended capture probes (e.g., DNA molecules) act as templates for an amplification reaction (e.g., a polymerase chain reaction).

Additional variants of spatial analysis methods, including in some embodiments, an imaging step, are described in Section (II)(a) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663. Analysis of captured analytes (and/or intermediate agents or portions thereof), for example, including sample removal, extension of capture probes, sequencing (e.g., of a cleaved extended capture probe and/or a cDNA molecule complementary to an extended capture probe), sequencing on the array (e.g., using, for example, in situ hybridization or in situ ligation approaches), temporal analysis, and/or proximity capture, is described in Section (II)(g) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663. Some quality control measures are described in Section (II)(h) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663.

Spatial information can provide information of biological and/or medical importance. For example, the methods and compositions described herein can allow for: identification of one or more biomarkers (e.g., diagnostic, prognostic, and/or for determination of efficacy of a treatment) of a disease or disorder; identification of a candidate drug target for treatment of a disease or disorder; identification (e.g., diagnosis) of a subject as having a disease or disorder; identification of stage and/or prognosis of a disease or disorder in a subject; identification of a subject as having an increased likelihood of developing a disease or disorder; monitoring of progression of a disease or disorder in a subject; determination of efficacy of a treatment of a disease or disorder in a subject; identification of a patient subpopulation for which a treatment is effective for a disease or disorder; modification of a treatment of a subject with a disease or disorder; selection of a subject for participation in a clinical trial; and/or selection of a treatment for a subject with a disease or disorder.

Spatial information can provide information of biological importance. For example, the methods and compositions described herein can allow for: identification of transcriptome and/or proteome expression profiles (e.g., in healthy and/or diseased tissue); identification of multiple analyte types in close proximity (e.g., nearest neighbor analysis); determination of up- and/or down-regulated genes and/or proteins in diseased tissue; characterization of tumor microenvironments; characterization of tumor immune responses; characterization of cells types and their co-localization in tissue; and identification of genetic variants within tissues (e.g., based on gene and/or protein expression profiles associated with specific disease or disorder biomarkers).

Typically, for spatial array-based methods, a substrate functions as a support for direct or indirect attachment of capture probes to features of the array. A “feature” is an entity that acts as a support or repository for various molecular entities used in spatial analysis. In some embodiments, some or all of the features in an array are functionalized for analyte capture. Exemplary substrates are described in Section (II)(c) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663. Exemplary features and geometric attributes of an array can be found in Sections (II)(d)(i), (II)(d)(iii), and (II)(d)(iv) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663.

Generally, analytes and/or intermediate agents (or portions thereof) can be captured when contacting a biological sample with a substrate including capture probes (e.g., a substrate with capture probes embedded, spotted, printed, fabricated on the substrate, or a substrate with features (e.g., beads, wells) comprising capture probes). As used herein, “contact,” “contacted,” and/or “contacting,” a biological sample with a substrate refers to any contact (e.g., direct or indirect) such that capture probes can interact (e.g., bind covalently or non-covalently (e.g., hybridize)) with analytes from the biological sample. Capture can be achieved actively (e.g., using electrophoresis) or passively (e.g., using diffusion). Analyte capture is further described in Section (II)(e) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663.

In some cases, spatial analysis can be performed by attaching and/or introducing a molecule (e.g., a peptide, a lipid, or a nucleic acid molecule) having a barcode (e.g., a spatial barcode) to a biological sample (e.g., to a cell in a biological sample). In some embodiments, a plurality of molecules (e.g., a plurality of nucleic acid molecules) having a plurality of barcodes (e.g., a plurality of spatial barcodes) are introduced to a biological sample (e.g., to a plurality of cells in a biological sample) for use in spatial analysis. In some embodiments, after attaching and/or introducing a molecule having a barcode to a biological sample, the biological sample can be physically separated (e.g., dissociated) into single cells or cell groups for analysis. Some such methods of spatial analysis are described in Section (III) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663.

In some cases, spatial analysis can be performed by detecting multiple oligonucleotides that hybridize to an analyte. In some instances, for example, spatial analysis can be performed using RNA-templated ligation (RTL). Methods of RTL have been described previously. See, e.g., Credle et al., Nucleic Acids Res. 2017 Aug. 21; 45(14):e128. Typically, RTL includes hybridization of two oligonucleotides to adjacent sequences on an analyte (e.g., an RNA molecule, such as an mRNA molecule). In some instances, the oligonucleotides are DNA molecules. In some instances, one of the oligonucleotides includes at least two ribonucleic acid bases at the 3′ end and/or the other oligonucleotide includes a phosphorylated nucleotide at the 5′ end. In some instances, one of the two oligonucleotides includes a capture domain (e.g., a poly(A) sequence, a non-homopolymeric sequence). After hybridization to the analyte, a ligase (e.g., SplintR ligase) ligates the two oligonucleotides together, creating a ligation product. In some instances, the two oligonucleotides hybridize to sequences that are not adjacent to one another. For example, hybridization of the two oligonucleotides creates a gap between the hybridized oligonucleotides. In some instances, a polymerase (e.g., a DNA polymerase) can extend one of the oligonucleotides prior to ligation. After ligation, the ligation product is released from the analyte. In some instances, the ligation product is released using an endonuclease (e.g., RNAse H). The released ligation product can then be captured by capture probes (e.g., instead of direct capture of an analyte) on an array, optionally amplified, and sequenced, thus determining the location and optionally the abundance of the analyte in the biological sample.

During analysis of spatial information, sequence information for a spatial barcode associated with an analyte is obtained, and the sequence information can be used to provide information about the spatial distribution of the analyte in the biological sample. Various methods can be used to obtain the spatial information. In some embodiments, specific capture probes and the analytes they capture are associated with specific locations in an array of features on a substrate. For example, specific spatial barcodes can be associated with specific array locations prior to array fabrication, and the sequences of the spatial barcodes can be stored (e.g., in a database) along with specific array location information, so that each spatial barcode uniquely maps to a particular array location.

Alternatively, specific spatial barcodes can be deposited at predetermined locations in an array of features during fabrication such that at each location, only one type of spatial barcode is present so that spatial barcodes are uniquely associated with a single feature of the array. Where necessary, the arrays can be decoded using any of the methods described herein so that spatial barcodes are uniquely associated with array feature locations, and this mapping can be stored as described above.

When sequence information is obtained for capture probes and/or analytes during analysis of spatial information, the locations of the capture probes and/or analytes can be determined by referring to the stored information that uniquely associates each spatial barcode with an array feature location. In this manner, specific capture probes and captured analytes are associated with specific locations in the array of features. Each array feature location represents a position relative to a coordinate reference point (e.g., an array location, a fiducial marker) for the array. Accordingly, each feature location has an “address” or location in the coordinate space of the array.

Some exemplary spatial analysis workflows are described in the Exemplary Embodiments section of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663. See, for example, the Exemplary embodiment starting with “In some non-limiting examples of the workflows described herein, the sample can be immersed . . . ” of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663. See also, e.g., the Visium Spatial Gene Expression Reagent Kits User Guide (e.g., Rev C, dated June 2020), and/or the Visium Spatial Tissue Optimization Reagent Kits User Guide (e.g., Rev C, dated July 2020).

In some embodiments, spatial analysis can be performed using dedicated hardware and/or software, such as any of the systems described in Sections (II)(e)(ii) and/or (V) of WO 2020/176788 and/or U.S. Patent Application Publication No. 2020/0277663, or any of one or more of the devices or methods described in Sections Control Slide for Imaging, Methods of Using Control Slides and Substrates for, Systems of Using Control Slides and Substrates for Imaging, and/or Sample and Array Alignment Devices and Methods, Informational labels of WO 2020/123320.

Suitable systems for performing spatial analysis can include components such as a chamber (e.g., a flow cell or sealable, fluid-tight chamber) for containing a biological sample. The biological sample can be mounted for example, in a biological sample holder. One or more fluid chambers can be connected to the chamber and/or the sample holder via fluid conduits, and fluids can be delivered into the chamber and/or sample holder via fluidic pumps, vacuum sources, or other devices coupled to the fluid conduits that create a pressure gradient to drive fluid flow. One or more valves can also be connected to fluid conduits to regulate the flow of reagents from reservoirs to the chamber and/or sample holder.

The systems can optionally include a control unit that includes one or more electronic processors, an input interface, an output interface (such as a display), and a storage unit (e.g., a solid state storage medium such as, but not limited to, a magnetic, optical, or other solid state, persistent, writeable and/or re-writeable storage medium). The control unit can optionally be connected to one or more remote devices via a network. The control unit (and components thereof) can generally perform any of the steps and functions described herein. Where the system is connected to a remote device, the remote device (or devices) can perform any of the steps or features described herein. The systems can optionally include one or more detectors (e.g., CCD, CMOS) used to capture images. The systems can also optionally include one or more light sources (e.g., LED-based, diode-based, lasers) for illuminating a sample, a substrate with features, analytes from a biological sample captured on a substrate, and various control and calibration media.

The systems can optionally include software instructions encoded and/or implemented in one or more of tangible storage media and hardware components such as application specific integrated circuits. The software instructions, when executed by a control unit (and in particular, an electronic processor) or an integrated circuit, can cause the control unit, integrated circuit, or other component executing the software instructions to perform any of the method steps or functions described herein.

In some cases, the systems described herein can detect (e.g., register an image) the biological sample on the array. Exemplary methods to detect the biological sample on an array are described in PCT Application No. 2020/061064 and/or U.S. patent application Ser. No. 16/951,854.

Prior to transferring analytes from the biological sample to the array of features on the substrate, the biological sample can be aligned with the array. Alignment of a biological sample and an array of features including capture probes can facilitate spatial analysis, which can be used to detect differences in analyte presence and/or level within different positions in the biological sample, for example, to generate a three-dimensional map of the analyte presence and/or level. Exemplary methods to generate a two- and/or three-dimensional map of the analyte presence and/or level are described in PCT Application No. 2020/053655 and spatial analysis methods are generally described in WO 2020/061108 and/or U.S. patent application Ser. No. 16/951,864.

In some cases, a map of analyte presence and/or level can be aligned to an image of a biological sample using one or more fiducial markers, e.g., objects placed in the field of view of an imaging system which appear in the image produced, as described in the Substrate Attributes Section, Control Slide for Imaging Section of WO 2020/123320, PCT Application No. 2020/061066, and/or U.S. patent application Ser. No. 16/951,843. Fiducial markers can be used as a point of reference or measurement scale for alignment (e.g., to align a sample and an array, to align two substrates, to determine a location of a sample or array on a substrate relative to a fiducial marker) and/or for quantitative measurements of sizes and/or distances.

Methods for Reducing Unwanted Target Nucleic Acid Capture or Proxies Thereof on an Array

Spatial arrays provide researchers the tools to identify gene expression, protein locations, and/or other cellular activity in a spatial manner. The benefits of correlating spatial biological relationships with diseases and disorders does, and will, continue to advance many fields of scientific study. However, improvements in the resolution of spatial relationships between cellular activities and diseases and disorders would enhance those data. For example, when a biological sample (e.g., a tissue section) placed on a spatial array is permeabilized to release target nucleic acids, some of the nucleic acids from the biological sample can, via diffusion, move to areas of the array where there is no biological sample (e.g., tissue section), for example adjacent to or not covered by the biological sample, where unwanted nucleic acid analyte capture can occur. This type of unwanted nucleic acid or proxy thereof capture can decrease the resolution of the desired spatial data. Further, unwanted nucleic acid capture can cause downstream sequencing inefficiencies; a decrease in the amount of target nucleic acid sequencing due to sequencing of unwanted captured nucleic acids or proxies thereof is inefficient and reagent costly. The present disclosure provides solutions for improving and/or preventing unwanted nucleic acid capture on an array on areas adjacent to and/or not covered by the biological sample.

FIG. 1 is a schematic diagram showing an exemplary capture probe, as described herein. As shown, the capture probe 102 is optionally coupled to a feature 101 by a cleavage domain 103, such as a disulfide linker. The capture probe can include a functional sequence 104 that are useful for subsequent processing. The functional sequence 104 can include all or a part of sequencer specific flow cell attachment sequence (e.g., a P5 or P7 sequence), all or a part of a sequencing primer sequence, (e.g., a R1 primer binding site, a R2 primer binding site), or combinations thereof. The capture probe can also include a spatial barcode 105. The capture probe can also include a unique molecular identifier (UMI) sequence 106. While FIG. 1 shows the spatial barcode 105 as being located upstream (5′) of UMI sequence 106, it is to be understood that capture probes wherein UMI sequence 106 is located upstream (5′) of the spatial barcode 105 is also suitable for use in any of the methods described herein. The capture probe can also include a capture domain 107 to facilitate capture of a target analyte. In some embodiments, the capture probe comprises one or more additional functional sequences that can be located, for example between the spatial barcode 105 and the UMI sequence 106, between the UMI sequence 106 and the capture domain 107, or following the capture domain 107. The capture domain can have a sequence complementary to a sequence of a nucleic acid analyte. The capture domain can have a sequence complementary to a connected probe described herein. The capture domain can have a sequence complementary to a capture handle sequence present in an analyte capture agent. The capture domain can have a sequence complementary to a splint oligonucleotide. Such splint oligonucleotide, in addition to having a sequence complementary to a capture domain of a capture probe, can have a sequence of a nucleic acid analyte, a sequence complementary to a portion of a connected probe described herein, and/or a capture handle sequence described herein.

The functional sequences can generally be selected for compatibility with any of a variety of different sequencing systems, e.g., Ion Torrent Proton or PGM, Illumina sequencing instruments, PacBio, Oxford Nanopore, etc., and the requirements thereof. In some embodiments, functional sequences can be selected for compatibility with non-commercialized sequencing systems. Examples of such sequencing systems and techniques, for which suitable functional sequences can be used, include (but are not limited to) Ion Torrent Proton or PGM sequencing, Illumina sequencing, PacBio SMRT sequencing, and Oxford Nanopore sequencing. Further, in some embodiments, functional sequences can be selected for compatibility with other sequencing systems, including non-commercialized sequencing systems.

In some embodiments, the spatial barcode 105 and functional sequences 104 is common to all of the probes attached to a given feature. In some embodiments, the UMI sequence 106 of a capture probe attached to a given feature is different from the UMI sequence of a different capture probe attached to the given feature.

The methods herein describe blocking a capture domain of one or more capture probes using terminal deoxynucleotidyl transferase (TdT) and one or more dideoxynucleotides. TdT can transfer one or more dideoxynucleotides to the 3′ hydroxyl end of the capture domain of a capture probe which prevents ligation or polymerase extension reactions (e.g., reverse transcription reactions).

In some embodiments, the methods herein describe blocking a capture domain of one or more capture probes by applying TdT and one or more dideoxynucleotides to the array prior to permeabilization of the biological sample. This can prevent extending the capture domain by reverse transcription of one or more capture probes that are not covered by the biological sample (e.g., in areas not covered by the biological sample). Blocking the capture domain can conserve resources, reduce wasted sequencing reads, and reduce mislocalized transcripts that appear in voids or spaces or tears of tissue (e.g., airways that may be found in lung tissue sections).

Provided herein are methods for determining a location of a target nucleic acid in a biological sample, the method including: (a) disposing a biological sample onto an array at a first rea, where the array includes a plurality of capture probes, where: a first capture probe of the plurality of capture probes includes a spatial barcode and a capture domain, where the first capture probe is included in the first area of the array; and a second area of the array includes a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array; (b) contacting the second area of the array with a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are incorporated into the capture domain of the second capture probe; (c) removing residual solution from the second area of the array; (d) permeabilizing the biological sample, such that the capture domain of the first capture probe hybridizes to the target nucleic acid from the biological sample; and (e) determining (i) a sequence corresponding to the spatial barcode of the first capture probe, or a complement thereof, and (ii) all or a portion of a sequence corresponding to the target nucleic acid, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.

Also provided herein are methods of blocking capture probes not covered by a biological sample, the method including: (a) disposing a biological sample onto an array at a first area, where the array includes a plurality of capture probes, where: a first capture probe of the plurality of capture probes includes a spatial barcode and a capture domain, where the first capture probe is included in the first area of the array; and a second area of the array includes a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array; and (b) contacting the second area of the array with a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are incorporated into the capture domain of the second capture probe in the second area.

In some embodiments, a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is applied to the array to prevent barcode exchange that can result from capture probes acting as extension templates. For example, the solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides can be applied to the array after extending a 3′ end of the first capture probe and/or after generating a second strand of nucleic acid complementary to the cDNA.

In some embodiments, a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is applied to a biological sample on an array and removed prior to tissue permeabilization.

Also provided herein are methods for determining a location of a target nucleic acid in a biological sample, the method including: (a) disposing a biological sample onto an array at a first area, where the array includes a plurality of capture probes, where: a first capture probe of the plurality of capture probes includes a spatial barcode and a capture domain, where the first capture probe is included in the first area of the array; and a second area of the array includes a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array, where the capture domain of the first capture probe hybridizes to a ligation product; (b) extending the ligation product toward the 5′ end of the first capture probe using the first capture probe as a template; (c) contacting the second area of the array with a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are incorporated into the capture domain of the second capture probe; (d) removing residual solution from the second area of the array; and (e) determining (i) a sequence corresponding to the spatial barcode of the first capture probe, or a complement thereof, and (ii) all or a portion of a sequence corresponding to the ligation product, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.

Also provided herein are methods of blocking capture probes to decrease barcode exchange and/or decrease the use of capture probes as extension templates, the method including: (a) disposing a biological sample onto an array at a first area, where the array includes a plurality of capture probes, where: a first capture probe of the plurality of capture probes includes a spatial barcode and a capture domain, where the first capture probe is included in the first area of the array; and a second area of the array includes a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array, where the capture domain of the first capture probe hybridizes to a ligation product; (b) extending the ligation product toward the 5′ end of the first capture probe using the first capture probe as a template; and (c) contacting the second area of the array with a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are incorporated into the capture domain of the second capture probe.

The biological sample can be any of the biological samples described herein. For example, in some embodiments, the biological sample is a tissue sample. In some embodiments, the tissue sample is a fresh-frozen tissue sample. In some embodiments, the tissue sample is a fixed tissue sample (e.g., fixed by any of the fixatives described herein). In some embodiments, the biological sample is a tissue section. In some embodiments, the tissue section is a fresh-frozen tissue section. In some embodiments, the tissue section is a fixed tissue section (e.g., fixed by any of the fixatives described herein). In other embodiments, the biological sample is a clinical sample (e.g., whole blood, blood cells, cultured tissue, cultured cells, or a cell suspension). In some embodiments, the biological sample is an organoid, embryonic stem cells, pluripotent stem cells, or any combination thereof. Non-limiting examples of an organoid include a cerebral organoid, an intestinal organoid, a stomach organoid, a lingual organoid, a thyroid organoid, a thymic organoid, a testicular organoid, a hepatic organoid, a pancreatic organoid, an epithelial organoid, a lung organoid, a kidney organoid, a gastruloid, a cardiac organoid, a retinal organoid, or any combination thereof. In other example embodiments, the biological sample can include diseased cells, fetal cells, immune cells, cellular macromolecules, organelles, extracellular polynucleotides, or any combination thereof.

Non-limiting examples of a target nucleic acid include DNA analytes such as genomic DNA, methylated DNA, specific methylated DNA sequences, fragmented DNA, mitochondrial DNA, in situ synthesized PCR products, and viral DNA.

Non-limiting examples of a target nucleic acid also include RNA analytes such as various types of coding and non-coding RNA. Examples of the different types of RNA analytes include messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), microRNA (miRNA), and viral RNA. The RNA can be a transcript (e.g., present in a tissue section). The RNA can be small (e.g., less than 200 nucleic acid bases in length) or large (e.g., RNA greater than 200 nucleic acid bases in length). Small RNAs mainly include 5.8S ribosomal RNA (rRNA), 5S rRNA, transfer RNA (tRNA), microRNA (miRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNAs), Piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA), and small rDNA-derived RNA (srRNA). The RNA can be double-stranded RNA or single-stranded RNA. The RNA can be circular RNA. The RNA can be a bacterial rRNA (e.g., 16s rRNA or 23s rRNA). The RNA can be from an RNA virus, for example RNA viruses from Group III, IV or V of the Baltimore classification system. The RNA can be from a retrovirus, such as a virus from Group VI of the Baltimore classification system.

In some embodiments, the target nucleic acid can include at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 disease-causing mutations (e.g., cancer-causing mutations). In some embodiments, the target nucleic acid includes a single nucleotide polymorphism, gene amplification, or chromosomal translocation, deletion or insertion.

In some embodiments, the method includes removing the residual solution (e.g., washing the array using any of the methods for removing solutions described herein) from the biological sample prior to permeabilization. In some embodiments, the biological sample can be fixed (e.g., the biological sample can be fixed using any of the techniques described herein or known in the art). In some embodiments, fixing the biological sample includes the use of a fixative such as ethanol, methanol, acetone, formaldehyde, formalin, paraformaldehyde-Triton, glutaraldehyde, or any combination thereof. In some embodiments, a fixed biological sample is a formalin-fixed paraffin-embedded tissue sample. In some embodiments, a fixed biological sample is a formalin-fixed paraffin-embedded tissue section. In some embodiments, the biological sample can be fixed (e.g., after step (a), or between steps (a) and (b), the biological sample can be fixed using any of the techniques described herein or known in the art).

In some embodiments, the biological sample can be stained and/or imaged using any of the techniques described herein or known in the art (e.g., the biological sample can be stained and/or imaged after step (a), or between steps (a) and (b)). In some embodiments, staining includes optical labels as described herein, including, but not limited to, fluorescent (e.g., fluorophore), radioactive (e.g., radioisotope), chemiluminescent (e.g., a chemiluminescent compound), a bioluminescent compound, calorimetric, or colorimetric detectable labels. In some embodiments, staining includes a fluorescent antibody directed to a target analyte (e.g., cell surface or intracellular proteins) in the biological sample. In some embodiments, staining includes an immunohistochemistry stain directed to a target analyte (e.g., cell surface or intracellular proteins) in the biological sample. In some embodiments, staining includes a chemical stain, such as hematoxylin and eosin (H&E) or periodic acid-schiff (PAS). In some embodiments, staining the biological sample includes the use of a biological stain including, but not limited to, acridine orange, Bismarck brown, carmine, coomassie blue, cresyl violet, DAPI, eosin, ethidium bromide, acid fuchsine, hematoxylin, Hoechst stains, iodine, methyl green, methylene blue, neutral red, Nile blue, Nile red, osmium tetroxide, propidium iodide, rhodamine, safranin, or any combination thereof. In some embodiments, significant time (e.g., days, months, or years) can elapse between staining and/or imaging the biological sample.

In some embodiments, the determining includes extending a 3′ end of the capture probe of the first area of the array using the target nucleic acid as a template. In some embodiments, the determining includes sequencing (i) the spatial barcode of the first capture probe of the array, or a complement thereof, and (ii) all or a portion of the target nucleic acid, or a complement thereof. In some embodiments, the determining includes sequencing (i) the spatial barcode of the first capture probe of the array, or a complement thereof, and (ii) all or a portion of a ligation product, or a complement thereof.

In some embodiments, permeabilizing the biological sample includes contacting the biological sample with a permeabilization agent. In some embodiments, the permeabilization agent includes the use of an organic solvent, a detergent, an enzyme, or combinations thereof. The permeabilization agent can include: an endopeptidase, a protease, sodium dodecyl sulfate (SDS), polyethylene glycol tert-octylphenyl ether, polysorbate 80, and polysorbate 20, N-lauroylsarcosine sodium salt solution, saponin, Triton X-100™, and Tween-20™. In some embodiments, the endopeptidase is pepsin or proteinase K.

In some embodiments, the biological sample is imaged prior to permeabilization.

First and Second Areas

In some embodiments of any of the methods described herein, an array can have a first area upon which a biological sample is disposed and a second area that is adjacent to (e.g., not covered by) the biological sample. For instance, some embodiments of any of the methods described herein include disposing a biological sample onto an array (e.g., any of the exemplary arrays described herein), where the array has a first area covered by the biological sample and a second area not covered by the biological sample.

In some examples, the first area can represent a portion of the array that is covered by the biological sample, e.g., about 10% to about 99%, about 10% to about 95%, about 10% to about 90%, about 10% to about 85%, about 10% to about 80%, about 10% to about 75%, about 10% to about 70%, about a 10% to about 65%, about 10% to about 60%, about 10% to about 55%, about 10% to about 50%, about 10% to about 45%, about 10% to about 40%, about 10% to about 35%, about 10% to about 30%, about 10% to about 25%, about 10% to about 20%, about 10% to about 15%, about 15% to about 99%, about 15% to about 95%, about 15% to about 90%, about 15% to about 85%, about 15% to about 80%, about 15% to about 75%, about 15% to about 70%, about a 15% to about 65%, about 15% to about 60%, about 15% to about 55%, about 15% to about 50%, about 15% to about 45%, about 15% to about 40%, about 15% to about 35%, about 15% to about 30%, about 15% to about 25%, about 15% to about 20%, about 20% to about 99%, about 20% to about 95%, about 20% to about 90%, about 20% to about 85%, about 20% to about 80%, about 20% to about 75%, about 20% to about 70%, about a 20% to about 65%, about 20% to about 60%, about 20% to about 55%, about 20% to about 50%, about 20% to about 45%, about 20% to about 40%, about 20% to about 35%, about 20% to about 30%, about 20% to about 25%, about 25% to about 99%, about 25% to about 95%, about 25% to about 90%, about 25% to about 85%, about 25% to about 80%, about 25% to about 75%, about 25% to about 70%, about a 25% to about 65%, about 25% to about 60%, about 25% to about 55%, about 25% to about 50%, about 25% to about 45%, about 25% to about 40%, about 25% to about 35%, about 25% to about 30%, about 30% to about 99%, about 30% to about 95%, about 30% to about 90%, about 30% to about 85%, about 30% to about 80%, about 30% to about 75%, about 30% to about 70%, about a 30% to about 65%, about 30% to about 60%, about 30% to about 55%, about 30% to about 50%, about 30% to about 45%, about 30% to about 40%, about 30% to about 35%, about 35% to about 99%, about 35% to about 95%, about 35% to about 90%, about 35% to about 85%, about 35% to about 80%, about 35% to about 75%, about 35% to about 70%, about a 35% to about 65%, about 35% to about 60%, about 35% to about 55%, about 35% to about 50%, about 35% to about 45%, about 35% to about 40%, about 40% to about 99%, about 40% to about 95%, about 40% to about 90%, about 40% to about 85%, about 40% to about 80%, about 40% to about 75%, about 40% to about 70%, about a 40% to about 65%, about 40% to about 60%, about 40% to about 55%, about 40% to about 50%, about 40% to about 45%, about 45% to about 99%, about 45% to about 95%, about 45% to about 90%, about 45% to about 85%, about 45% to about 80%, about 45% to about 75%, about 45% to about 70%, about a 45% to about 65%, about 45% to about 60%, about 45% to about 55%, about 45% to about 50%, about 50% to about 99%, about 50% to about 95%, about 50% to about 90%, about 50% to about 85%, about 50% to about 80%, about 50% to about 75%, about 50% to about 70%, about a 50% to about 65%, about 50% to about 60%, about 50% to about 55%, about 55% to about 99%, about 55% to about 95%, about 55% to about 90%, about 55% to about 85%, about 55% to about 80%, about 55% to about 75%, about 55% to about 70%, about a 55% to about 65%, about 55% to about 60%, about 60% to about 99%, about 60% to about 95%, about 60% to about 90%, about 60% to about 85%, about 60% to about 80%, about 60% to about 75%, about 60% to about 70%, about a 60% to about 65%, about 65% to about 99%, about 65% to about 95%, about 65% to about 90%, about 65% to about 85%, about 65% to about 80%, about 65% to about 75%, about 65% to about 70%, about 70% to about 99%, about 70% to about 95%, about 70% to about 90%, about 70% to about 85%, about 70% to about 80%, about 70% to about 75%, about 75% to about 99%, about 75% to about 95%, about 75% to about 90%, about 75% to about 85%, about 75% to about 80%, about 80% to about 99%, about 80% to about 95%, about 80% to about 90%, about 80% to about 85%, about 85% to about 99%, about 85% to about 95%, about 85% to about 90%, about 90% to about 99%, about 90% to about 95%, or about 95% to about 99%, of the total area of the array covered by the biological sample.

The second area represents a portion of the array that is not covered by the biological sample.

Solution of Terminal Deoxynucleotidyl Transferase and One or More Dideoxynucleotides

The solution of terminal deoxynucleotidyl transferase and one or more dideoxynucleotides can include a buffer. In some embodiments, the solution includes about 0.5 mM of the dideoxynucleotides to about 25 mM of the dideoxynucleotides (e.g., about 0.5 mM to about 24.5 mM, about 0.5 mM to about 24 mM, about 0.5 mM to about 23.5 mM, about 0.5 mM to about 23 mM, about 0.5 mM to about 22.5 mM, about 0.5 mM to about 22 mM, about 0.5 mM to about 21.5 mM, about 0.5 mM to about 21 mM, about 0.5 mM to about 20.5 mM, about 0.5 mM to about 20 mM, about 0.5 mM to about 19.5 mM, about 0.5 mM to about 19 mM, about 0.5 mM to about 18.5 mM, about 0.5 mM to about 18 mM, about 0.5 mM to about 17.5 mM, about 0.5 mM to about 17 mM, about 0.5 mM to about 16.5 mM, about 0.5 mM to about 16 mM, about 0.5 mM to about 15.5 mM, about 0.5 mM to about 15 mM, about 0.5 mM to about 14.5 mM, about 0.5 mM to about 14 mM, about 0.5 mM to about 13.5 mM, about 0.5 mM to about 13 mM, about 0.5 mM to about 12.5 mM, about 0.5 mM to about 12 mM, about 0.5 mM to about 11.5 mM, about 0.5 mM to about 11 mM, about 0.5 mM to about 10.5 mM, about 0.5 mM to about 10 mM, about 0.5 mM to about 9.5 mM, about 0.5 mM to about 9 mM, about 0.5 mM to about 8.5 mM, about 0.5 mM to about 8 mM, about 0.5 mM to about 7.5 mM, about 0.5 mM to about 7 mM, about 0.5 mM to about 6.5 mM, about 0.5 mM to about 6 mM, about 0.5 mM to about 5.5 mM, about 0.5 mM to about 5 mM, about 0.5 mM to about 4.5 mM, about 0.5 mM to about 4 mM, about 0.5 mM to about 3.5 mM, about 0.5 mM to about 3 mM, about 0.5 mM to about 2.5 mM, about 0.5 mM to about 2 mM, about 0.5 mM to about 1.5 mM, or about 0.5 mM to about 1 mM). In some embodiments, the buffer is a reaction buffer. In some embodiments, the solution includes about 0.02 mM to about 2.0 mM of the dideoxynucleotides. In some embodiments, the solution includes about 1 mM of the dideoxynucleotides. In some embodiments, the dideoxynucleotide is ddATP and/or ddTTP. In some embodiments, the dideoxynucleotide is ddCTP and/or ddGTP. In some embodiments, the dideoxynucleotides include a mixture of ddATP, ddTTP, ddCTP, and ddGTP.

In some embodiments, the solution of terminal deoxynucleotidyl transferase and one or more dideoxynucleotides can include CoCl₂. In some embodiments, the solution includes about 0.1 mM CoCl₂ to about 2 mM CoCl₂, (e.g., about 0.1 mM to about 1.8 mM, about 0.1 mM to about 1.6 mM, about 0.1 mM to about 1.4 mM, about 0.1 mM to about 1.2 mM, about 0.1 mM to about 1.0 mM, about 0.1 mM to about 0.8 mM, about 0.1 mM to about 0.6 mM, about 0.1 mM to about 0.4 mM, or about 0.1 mM to about 0.2 mM). In some embodiments, the solution includes about 0.25 mM CoCl₂. Other divalent cationic cofactors such as Mg⁺², Mn⁺², and Zn⁺² (e.g., salts of the divalent cations) can also be utilized by the TdT enzyme. A skilled artisan will understand that the rate of the enzymatic activity of TdT can depend upon one or both of the nucleotide and/or the cofactor being used in the reaction.

Contacting the Second Area of the Array with a Solution Including Terminal Deoxynucleotidyl Transferase and One or More Dideoxynucleotides

In some embodiments, the solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is added automatically (e.g., by a device e.g., a robot) or manually (e.g., by pipetting) to the second area of the array. In some embodiments, the solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is added dropwise by a pipette. In some embodiments, the solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is added to contact all or a portion of the second area of the array. In some embodiments, the solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is added to all or a portion of a surface of the biological sample that is not facing or contacting the array. In some embodiments, the solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is added to the whole array.

In some embodiments, the solution is added vertically above the second area of the array. In some embodiments, the solution is present in liquid form, such that the second area is covered by the solution.

In some embodiments, the second area of the array can be contacted by the solution for, e.g., about 5 minutes to about 90 minutes, about 5 minutes to about 80 minutes, about 5 minutes to about 70 minutes, about 5 minutes to about 60 minutes, about 5 minutes to about 50 minutes, about 5 minutes to about 40 minutes, about 5 minutes to about 30 minutes, about 5 minutes to about 20 minutes, about 5 minutes to about 10 minutes, about 10 minutes to about 1 hour, about 10 minutes to about 50 minutes, about 10 minutes to about 40 minutes, about 10 minutes to about 30 minutes, about 10 minutes to about 20 minutes, about 20 minutes to about 1 hour, about 20 minutes to about 50 minutes, about 20 minutes to about 40 minutes, about 20 minutes to about 30 minutes, about 30 minutes to about 1 hour, about 30 minutes to about 50 minutes, about 30 minutes to about 40 minutes, about 40 minutes to about 1 hour, about 40 minutes to about 50 minutes, or about 50 minutes to about 1 hour. In some embodiments, the contacting step is performed for about 60 minutes.

In some embodiments, the contacting step is performed at a temperature of about 4° C. to about 45° C., about 4° C. to about 40° C., about 4° C. to about 35° C., about 4° C. to about 30° C., about 4° C. to about 25° C., about 4° C. to about 20° C., about 4° C. to about 15° C., about 4° C. to about 10° C., about 10° C. to about 45° C., about 10° C. to about 40° C., about 10° C. to about 35° C., about 10° C. to about 30° C., about 10° C. to about 25° C., about 10° C. to about 20° C., about 10° C. to about 15° C., about 15° C. to about 45° C., about 15° C. to about 40° C., about 15° C. to about 35° C., about 15° C. to about 30° C., about 15° C. to about 25° C., about 15° C. to about 20° C., about 20° C. to about 45° C., about 20° C. to about 40° C., about 20° C. to about 35° C., about 20° C. to about 30° C., about 20° C. to about 25° C., about 25° C. to about 45° C., about 25° C. to about 40° C., about 25° C. to about 35° C., about 25° C. to about 30° C., or about 30° C. to about 45° C. In some embodiments, the contacting step is performed at a temperature of about 25° C. to about 45° C. In some embodiments, the contacting step is performed at a temperature of about 37° C.

Removing the Solution Including Terminal Deoxynucleotidyl Transferase and One or More Dideoxynucleotides from the Second Area of the Array

In some embodiments, the solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is removed by pipetting. In some embodiments, the solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is removed by wicking (e.g., by an absorption paper). In some embodiments, the solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is removed by washing (e.g., using a wash buffer). In some embodiments, a wash buffer can be added to contact the first and/or second area of the array then removed by pipetting, wicking, or other methods known in the art. In some embodiments, a combination of removing methods can be used. In some embodiments, contacting and removing steps can be repeated (e.g., at least 2 times, 3 times, 4 times, or more). In some embodiments, a drying step can be performed after washing (e.g., air drying).

In some embodiments, the wash buffer is added automatically (e.g., by a robot) or manually (e.g., by pipetting). In some embodiments, the wash buffer is added vertically above the array. In some embodiments, the wash buffer is added vertically above the second area of the array. In some embodiments, the wash buffer is added dropwise by a pipette. In some embodiments, the wash buffer is added to contact all or a portion of the second area of the array. In some embodiments, the wash buffer is added to all or a portion of a surface of the biological sample that is not facing or contacting the array. In some embodiments, a wash buffer is added to the whole array including the first and second areas. In some embodiments, the washing buffer is 1×TE buffer, 1×TAE buffer, 1×TBE buffer, sodium saline citrate, or PBS. In some embodiments, the wash buffer contains a buffer (e.g., Tris, MOPS, HEPES, MES, or any other buffer known in the art), chelating agents (e.g., ethylenediaminetetraacetic acid (EDTA)), and/or metal ions (e.g., Mg²⁺). In some embodiments, the wash buffer can have a pH that is about 5.0, about 5.5, about 6.0, about 6.5, about 7.0, about 7.5, about 8.0, about 8.5, about 9.0, about 9.5, or about 10.0, or about 5.0 to 5.5, about 5.5 to 6.0, about 6.0 to 6.5, about 6.5 to 7.0, about 7.0 to 7.5, about 7.5 to 8.0, about 8.0 to 8.5, about 8.5 to 9.0, about 9.0 to 9.5, or about 9.5 to 10.0.

In some embodiments, the second area of the array is contacted by the wash buffer for about 5 seconds to about 1 hour, about 5 seconds to about 50 minutes, about 5 seconds to about 40 minutes, about 5 seconds to about 30 minutes, about 5 seconds to about 20 minutes, about 5 seconds to about 10 minutes, about 5 seconds to about 5 minutes, about 5 seconds to about 1 minute, about 5 seconds to about 30 seconds, about 5 seconds to about 10 seconds, about 10 seconds to about 1 hour, about 10 seconds to about 50 minutes, about 10 seconds to about 40 minutes, about 10 seconds to about 30 minutes, about 10 seconds to about 20 minutes, about 10 seconds to about 10 minutes, about 10 seconds to about 5 minutes, about seconds to about 1 minute, about 10 seconds to about 30 seconds, about 30 seconds to about 1 hour, about 30 seconds to about 50 minutes, about 30 seconds to about 40 minutes, about 30 seconds to about 30 minutes, about 30 seconds to about 20 minutes, about 30 seconds to about 10 minutes, about 30 seconds to about 5 minutes, about 30 seconds to about 1 minute, about 1 minute to about 1 hour, about 1 minute to about 50 minutes, about 1 minute to about 40 minutes, about 1 minute to about 30 minutes, about 1 minute to about 20 minutes, about 1 minute to about 10 minutes, about 1 minute to about 5 minutes, about 5 minutes to about 1 hour, about 5 minutes to about 50 minutes, about 5 minutes to about 40 minutes, about 5 minutes to about 30 minutes, about 5 minutes to about 20 minutes, about 5 minutes to about 10 minutes, about 10 minutes to about 1 hour, about 10 minutes to about 50 minutes, about 10 minutes to about 40 minutes, about 10 minutes to about 30 minutes, about 10 minutes to about 20 minutes, about 20 minutes to about 1 hour, about 20 minutes to about 50 minutes, about 20 minutes to about 40 minutes, about 20 minutes to about 30 minutes, about 30 minutes to about 1 hour, about 30 minutes to about 50 minutes, about 30 minutes to about 40 minutes, about 40 minutes to about 1 hour, about 40 minutes to about 50 minutes, or about 50 minutes to about 1 hour, at a temperature of about 4° C. to about 35° C., about 4° C. to about 30° C., about 4° C. to about 25° C., about 4° C. to about 20° C., about 4° C. to about 15° C., about 4° C. to about 10° C., about 10° C. to about 35° C. to about 10° C. to about 30° C., about 10° C. to about 25° C., about 10° C. to about 20° C., about 10° C. to about 15° C., about 15° C. to about 35° C., about 15° C. to about 30° C., about 15° C. to about 25° C., about 15° C. to about 20° C., about 20° C. to about 35° C., about 20° C. to about 30° C., about 20° to about 25° C., about 25° C. to about 35° C., about 25° C. to about 30° C., or about 30° C. to about 35° C.

Kits

Also provided herein are kits that include a solution including terminal deoxynucleotidyl transferase; one or more dideoxynucleotides, a substrate (e.g., an array) including a plurality of capture probes, where the capture probes include a spatial barcode and a capture domain; and instructions for performing any of the methods described herein.

In some embodiments, the kit can include one or more fixative(s) (e.g., any of the fixatives described herein) to fix the biological sample and/or preserve the structure of the biological sample. Non-limiting examples of a fixative include ethanol, methanol, acetone, formaldehyde (e.g., 2% formaldehyde), formalin, paraformaldehyde-Triton, glutaraldehyde, or any combination thereof.

In some embodiments, the kit includes about 0.5 mM of the dideoxynucleotides to about 25 mM of the dideoxynucleotides. In some embodiments, the dideoxynucleotide is ddATP. In some embodiments, the dideoxynucleotide is ddTTP. In some embodiments, the dideoxynucleotide is ddGTP. In some embodiments, the dideoxynucleotide is ddCTP. In some embodiments, the dideoxynucleotide is a mixture of ddATP, ddTTP, ddCTP, and ddGTP. In some embodiments, the solution includes about 0.5 mM of the dideoxynucleotide to about 1.5 mM of the dideoxynucleotide. In some embodiments, the solution includes about 1 mM of the dideoxynucleotide.

In some embodiments, the solution includes CoCl₂. In some embodiments, the solution includes about 0.1 mM CoCl₂ to about 2 mM CoCl₂. In some embodiments, the solution includes about 0.25 mM CoCl₂. In some embodiments, the solution includes about 0.1 mM to about 2 mM MgCl₂.

In some embodiments, the solution includes a buffer. In some embodiments, the kit includes a wash buffer including one or more of: a solvent, an acid, a base, and a buffer. In some embodiments, the wash buffer is phosphate buffered saline.

Compositions

The present disclosure also features compositions for blocking capture probes in an area (e.g., a second area) of an array not covered by a biological sample. Thus, provided herein are compositions including a biological sample disposed on an array at a first area, where the array includes a plurality of capture probes, wherein a first capture probe of the plurality of capture probes includes a spatial barcode and a capture domain, where the first capture probe is comprised in the first area of the array; where a second area of the array includes a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array; and a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides disposed on the second area of the array.

Also provided herein are compositions including a biological sample disposed on an array at a first area, where the first area includes a plurality of capture probes, where a first capture probe of the plurality of capture probes includes a spatial barcode and a capture domain, where the first capture probe is comprised in the first area of the array; a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides on a second area of the array; the second area of the array including a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array and the second capture probe in the second area is extended with one or more dideoxynucleotides.

Also provided herein are compositions including a an array including a first area and a second area, where the array includes a plurality of capture probes distributed across the first and second areas, where the first area includes a first capture probe of the plurality of capture probes including a spatial barcode and a capture domain; a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides disposed on the second area of the array; where the second area of the array includes a second capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second capture probe is extended with one or more dideoxynucleotides. In some embodiments of this composition, the first capture probe is hybridized to a target nucleic acid from a biological sample or a proxy thereof (e.g., a ligation product). In some embodiments of this composition, the first capture probe is extended (e.g., by ligation or reverse transcription) to further include the reverse complement of a target nucleic acid from a biological sample or a proxy thereof (e.g., a ligation product).

In some embodiments, the composition includes a wash buffer. In some embodiments, the wash buffer includes one or more of a solvent, an acid, a base, and a buffer. In some embodiments, the wash buffer includes phosphate buffered saline. In some embodiments, the wash buffer includes saline sodium citrate.

In some embodiments, the plurality of capture probes includes one or more functional domains, a cleavage domain, a unique molecular identifier, or a combination thereof.

In some embodiments, the composition includes an organic solvent, a detergent, an enzyme, or a combination thereof. In some embodiments, the composition includes a permeabilization agent, such as, but not limited to, an endopeptidase, a protease, sodium dodecyl sulfate, polyethylene glycol tert-octylphenyl ether, polysorbate 80, and polysorbate 20, N-lauroylsarcosine sodium salt solution, saponin, Triton X-100™, and Tween-20™. In some embodiments, the endopeptidase is pepsin. In some embodiments, the endopeptidase is proteinase K.

In some embodiments, the composition includes one or more fixatives. In some compositions, the fixative includes ethanol, methanol, acetone, formaldehyde, paraformaldehyde-Triton, glutaraldehyde, or a combination thereof. In some embodiments, the composition includes one or more stains. In some embodiments, the composition includes a hematoxylin and/or eosin stain. In some embodiments, the stain includes one or more of a detectable label selected from the group consisting of a radioisotope, a fluorophore, a chemiluminescent compound, a bioluminescent compound, or a combination thereof.

In some embodiments, the dideoxynucleotides include ddATP. In some embodiments, the dideoxynucleotides include ddTTP. In some embodiments, the dideoxynucleotides include ddGTP. In some embodiments, the dideoxynucleotides include ddCTP. In some embodiments, the dideoxynucleotides include a mixture of ddATP, ddTTP, ddCTP, and ddGTP. In some embodiments, the solution includes about 0.5 mM of the dideoxynucleotides to about 25 mM of the dideoxynucleotides. In some embodiments, the solution includes about 0.5 mM of the dideoxynucleotides to about 1.5 mM of the dideoxynucleotides. In some embodiments, the solution includes about 1 mM of the dideoxynucleotides.

In some embodiments, the solution includes CoCl₂. In some embodiments, the solution includes about 0.1 mM CoCl₂ to about 2 mM CoCl₂. In some embodiments, the solution includes about 0.25 mM CoCl₂. In some embodiments, the solution includes about 0.1 mM to about 2 mM MgCl₂.

In some embodiments, a capture probe of the first area is hybridized to a target nucleic acid. In some embodiments, the target nucleic acid is DNA. In some embodiments, the target nucleic acid is RNA. In some embodiments, the RNA is mRNA.

In some embodiments, a capture probe of the first area is hybridized to a ligation product (e.g., a ligation product as described herein). In some embodiments, the ligation product includes an analyte capture sequence. In some embodiments, the capture probe is hybridized to the analyte capture sequence of the ligation product.

EXAMPLES Example 1: A Method for Determining a Location of a Target Nucleic Acid in a Biological Sample

FIG. 2 is an exemplary workflow diagram 230 for a method of blocking the capture probes not covered by a biological sample on a spatial array and determining a location of a target nucleic acid in a biological sample. At 232 the exemplary method includes disposing a biological sample onto an array at a first area on the array, where the array includes a plurality of capture probes collectively across the first area and a second area. In the first area, a capture probe of the plurality of capture probes includes a spatial barcode and a capture domain. The second area is adjacent to the first area. For example, the second area is an area of the array not covered by the biological sample. The second area of the array also includes a capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is adjacent to the biological sample disposed on the array (e.g., not covered by the biological sample).

To block capture probes in the second area of the array, a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides is applied to the second area of the array. At 234, the exemplary method 230 describes contacting the array (e.g., the second area of the array) with a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are incorporated into the capture domain of the capture probes in the second area. For example, an exemplary solution including 1.5 μl of 1 mM ddATP, 7.5 μl of CoCl₂ at 0.25 mM, 7.5 μl 10× terminal deoxynucleotidyl transferase reaction buffer, water, and 6 μl terminal deoxynucleotidyl transferase at 1 U/μl terminal deoxynucleotidyl transferase (NEB) is added to an array and the array is incubated at 37° C. for about 30 minutes. However, it is understood that other deoxynucleotides and divalent cationic cofactors such as Mg+2, Mn+2, and Zn+2 (e.g., salts of the divalent cations) can also be utilized. After incubation, the residual solution is removed from the array. The residual solution is removed from the array by rinsing with a buffer. For example, if the biological sample is a fresh-frozen biological sample, the array is rinsed with 0.1× sodium saline citrate (SSC) buffer followed by water. If the biological sample is a fixed-formalin paraffin-embedded biological sample, the array is rinsed with 2×SSC followed by water.

Following removal of the solution, the biological sample is permeabilized. At 236, the exemplary method 230 includes permeabilizing the biological sample, such that the capture domain of the capture probe of the first area of the array hybridizes to the target nucleic acid from the biological sample.

A determination of a sequence corresponding to the spatial barcode of the capture probes in the first area is carried out. The sequence is generated with high throughput sequencing. At 238, the exemplary method 230 includes processing of the captured analyte by extending the 3′ end of the capture probe using the captured analyte as a temple to generate a first strand cDNA, generating a second strand cDNA that includes a copy of the first strand cDNA, the complement of the spatial barcode of the capture probe, and other sequences as found in the capture probe, library preparation of the second strand cDNA to generate a sequencing library and determining (i) a sequence corresponding to the spatial barcode of the capture probe of the first area of the array, or a complement thereof, and (ii) all or a portion of a sequence corresponding to the target nucleic acid, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.

The methods described in this example can also be used for the capture of proxies of analytes including, but not limited to ligation products (e.g., a ligation product as defined herein) and oligonucleotides including analyte-binding moiety barcodes and analyte capture sequences. For example, a ligation product can be a proxy for a target nucleic acid, where one or more probes hybridize to the target nucleic acid and at least one probe includes an analyte capture sequence that can hybridize to a capture domain of a capture probe. In some examples, when two probes hybridize to the target nucleic acid the two probes can be ligated to one another, thereby generating a ligation product (e.g., a proxy for the target nucleic acid). In other examples, oligonucleotides including analyte-binding moiety barcodes and analyte capture sequences can be conjugated to an analyte-binding moiety (e.g., an antibody or antigen-binding fragment thereof). The analyte capture sequence can hybridize to the capture domain of a capture probe and the analyte binding moiety barcode identifies the analyte (e.g., protein) bound by the analyte-binding moiety.

Example 2: A Method for Determining a Location of a Target Nucleic Acid in a Biological Sample

FIG. 3 is an exemplary workflow diagram 340 for a method of mitigating the possibility of capture probes acting as primers and determining a location of a target nucleic acid in a biological sample. At 342 the exemplary method includes disposing a biological sample onto an array at a first area on the array, where the array includes a plurality of capture probes collectively across the first area and a second area. In the first area, a capture probe of the plurality of capture probes includes a spatial barcode and a capture domain. The second area is adjacent to the first area. For example, the second area is an area of the array that is not covered by the biological sample. The second area of the array includes a capture probe of the plurality of capture probes including a spatial barcode and a capture domain, where the second area is not covered by the biological sample disposed on the array.

The biological sample is permeabilized 344 to allow the capture probe to hybridize to a target nucleic acid. At 344, the exemplary method 340 describes permeabilization of the biological sample and hybridization of the target nucleic acid, or proxy thereof, to the 3′ end of the capture probe (e.g., the capture domain) of the first area of the array. Incubation with extension reagents can produce spatially-barcoded DNA from the captured analytes.

At 346, the capture probes are extended on the array. Extension reagents (e.g., DNA polymerase and buffer) are added to the biological sample on the array to generate a cDNA (e.g., a second strand cDNA) containing a spatial barcode complementary to the capture probe of the array.

To prevent barcode exchange that results from capture probes acting as extension templates, a solution including terminal deoxynucleotidyl transferase can be added to the array (e.g., after first-strand probe extension e.g., reverse transcription). At 348, the exemplary method 340 includes contacting the second area of the array with a solution including terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are incorporated to the capture domain of the capture probes in the second area. An exemplary solution includes 1.5 μl of 100 mM ddATP, 7.5 μl of CoCl₂ at 0.25 mM, 7.5 μl 10× terminal deoxynucleotidyl transferase reaction buffer, water, and 6 μl terminal deoxynucleotidyl transferase at 1 U/μl terminal deoxynucleotidyl transferase (NEB). It is understood that other deoxynucleotides and divalent cationic cofactors such as Mg+2, Mn+2, and Zn+2 (e.g., salts of the divalent cations) can also be utilized. The solution is incubated on the array at 37° C. for 10 minutes. After incubation, the residual solution is removed from the array. The array is rinsed with 2× sodium saline citrate buffer.

A determination of a sequence corresponding to the spatial barcode, or a complement thereof, of the capture probes in the first area is determined. The sequence is generated with high throughput sequencing. At 350, the exemplary method 340 includes generating sequencing libraries from DNA probes and determining (i) a sequence corresponding to the spatial barcode of the capture probe of the first area of the array, or a complement thereof, and (ii) all or a portion of a sequence corresponding to the target nucleic acid, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.

The methods described in this example can also be used for the capture of a ligation product (e.g., a ligation product as defined herein). For example, a ligation product can be a proxy for a target nucleic acid, where one or more probes hybridize to the target nucleic acid, are ligated to one another, and at least one probe includes an analyte capture sequence that can hybridize to a capture domain of a capture probe.

Embodiments

Embodiment 1 is a method for determining a location of a target nucleic acid in a biological sample, the method comprising: (a) disposing a non-permeabilized biological sample onto an array at a first area, wherein the first area on the array comprises a plurality of capture probes, wherein: a capture probe of the plurality of capture probes comprises a spatial barcode and a capture domain; and a second area of the array comprising a capture probe of the plurality of capture probes comprises a spatial barcode and a capture domain, wherein the second area is adjacent to the biological sample disposed on the array; (b) contacting the second area of the array with a solution comprising terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are added to the capture domain of the capture probes; (c) removing the residual solution from the array; (d) permeabilizing the biological sample, such that the capture domain of the capture probe of the first area of the array binds to the target nucleic acid from the biological sample; and (e) determining (i) a sequence corresponding to the spatial barcode of the capture probe of the first area of the array, or a complement thereof, and (ii) all or a portion of a sequence corresponding to the target nucleic acid, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.

Embodiment 2 is the method of embodiment 1, wherein the removing step comprises the use of a wash buffer comprising one or more of: a solvent, an acid, a base, and a buffer.

Embodiment 3 is the method of embodiment 2, wherein the wash buffer comprises phosphate buffered saline or saline sodium citrate.

Embodiment 4 is the method of any one of embodiments 1-3, wherein the determining in step (d) comprises extending a 3′ end of the capture probe of the first area of the array using the target nucleic acid as a template.

Embodiment 5 is the method of any one of embodiments 1-4, wherein the determining in step (d) comprises sequencing (i) the spatial barcode of the capture probe of the first area of the array, or a complement thereof, and (ii) all or a portion of the target nucleic acid, or a complement thereof.

Embodiment 6 is the method of embodiment 5, wherein the sequencing is high throughput sequencing.

Embodiment 7 is the method of any one of embodiments 1-6, wherein the permeabilization agent is selected from an organic solvent, a detergent, and an enzyme, or a combination thereof.

Embodiment 8 is the method of embodiment 7, wherein the permeabilization agent is selected from the group consisting of: an endopeptidase, a protease sodium dodecyl sulfate, polyethylene glycol tert-octylphenyl ether, polysorbate 80, and polysorbate 20, N-lauroylsarcosine sodium salt solution, saponin, Triton X-100™, and Tween-20™.

Embodiment 9 is the method of embodiment 8, wherein the endopeptidase is pepsin or proteinase K.

Embodiment 10 is a method of blocking capture probes adjacent to a biological sample, the method comprising: (a) disposing a non-permeabilized biological sample onto an array at a first area, wherein the first area on the array comprises a plurality of capture probes, wherein: a capture probe of the plurality of capture probes comprises a spatial barcode and a capture domain; and a second area of the array comprising a capture probe of the plurality of capture probes comprises a spatial barcode and a capture domain, wherein the second area is adjacent to the biological sample disposed on the array; and (b) contacting the second area of the array with a solution comprising terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are added to the capture domain of the capture probes.

Embodiment 11 is the method of embodiment 10, wherein the method further comprises permeabilizing the biological sample, such that the capture domain of the capture probe of the first area of the array binds to the target nucleic acid from the biological sample.

Embodiment 12 is the method of embodiment 11, wherein step (c) comprises contacting the non-permeabilized biological sample with a permeabilization agent, wherein the permeabilization agent is selected from an organic solvent, a detergent, and an enzyme, or a combination thereof.

Embodiment 13 is the method of embodiment 12, wherein the permeabilization agent is selected from the group consisting of: an endopeptidase, a protease sodium dodecyl sulfate, polyethylene glycol tert-octylphenyl ether, polysorbate 80, and polysorbate 20, N-lauroylsarcosine sodium salt solution, saponin, Triton X-100™, and Tween-20™.

Embodiment 14 is the method of embodiment 13, wherein the endopeptidase is pepsin or proteinase K.

Embodiment 15 is the method of any one of embodiments 10-15, wherein the method further comprises removing the residual solution from the array prior to permeabilization.

Embodiment 16 is the method of embodiment 15, wherein the removing step comprises the use of a wash buffer comprising one or more of: a solvent, an acid, a base, and a buffer.

Embodiment 17 is the method of embodiment 16, wherein the wash buffer comprises phosphate buffered saline or saline sodium citrate.

Embodiment 18 is the method of any one of embodiments 1-17, wherein the non-permeabilized biological sample is fixed and/or stained prior to step (a).

Embodiment 19 is the method of any one of embodiments 1-18, wherein the method further comprises, between steps (a) and (b), fixing and/or staining the non-permeabilized biological sample.

Embodiment 20 is the method of embodiment 18 or embodiment 19, wherein the step of fixing the non-permeabilized biological sample comprises the use of a fixative selected from the group consisting of ethanol, methanol, acetone, formaldehyde, paraformaldehyde-Triton, glutaraldehyde, and combinations thereof.

Embodiment 21 is the method of embodiment 18 or embodiment 19, wherein the step of staining the non-permeabilized biological sample comprises the use of eosin and hematoxylin.

Embodiment 22 is the method of any one of embodiments 18-21, wherein the step of staining the non-permeabilized biological sample comprises the use of a detectable label selected from the group consisting of a radioisotope, a fluorophore, a chemiluminescent compound, a bioluminescent compound, or a combination thereof.

Embodiment 23 is a method for determining a location of a target nucleic acid in a biological sample, the method comprising: (a) disposing a biological sample onto an array at a first area on the array, wherein the first area on the array comprises a plurality of capture probes, wherein: a capture probe of the plurality of capture probes comprising a spatial barcode and a capture domain; and a second area of the array comprising a capture probe of the plurality of capture probes comprising a spatial barcode and a capture domain, wherein the second area is adjacent to the biological sample disposed on the array, wherein the capture domain of the capture probe of the first area of the array binds to the target nucleic acid; (b) extending a ligation product into the 5′ end of the capture probe of the first area of the array using the capture probe as a template; (c) contacting the second area of the array with a solution comprising terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are added to the capture domain of the capture probes; (d) removing the residual solution from the array; and (e) determining (i) a sequence corresponding to the spatial barcode of the capture probe of the first area of the array, or a complement thereof, and (ii) all or a portion of a sequence corresponding to the target nucleic acid, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.

Embodiment 24 is the method of embodiment 23, wherein the removing step comprises the use of a wash buffer comprising one or more of: a solvent, an acid, a base, and a buffer.

Embodiment 25 is the method of embodiment 24, wherein the wash buffer comprises phosphate buffered saline sodium citrate.

Embodiment 26 is the method of any one of embodiments 23-25, wherein the determining in step comprises extending a 3′ end of the capture probe of the first area of the array using the target nucleic acid as a template.

Embodiment 27 is the method of any one of embodiments 23-26, wherein the determining in step comprises sequencing (i) the spatial barcode of the capture probe of the first area of the array, or a complement thereof, and (ii) all or a portion of the target nucleic acid, or a complement thereof.

Embodiment 28 is the method of embodiment 27, wherein the sequencing is high throughput sequencing.

Embodiment 29 is a method of blocking capture probes to decrease barcode exchange and/or blocking capture probes to decrease the use of capture probes as primers, the method comprising: (a) disposing a biological sample onto an array at a first area on the array, wherein the first area on the array comprises a plurality of capture probes, wherein: a capture probe of the plurality of capture probes comprising a spatial barcode and a capture domain; and a second area of the array comprising a capture probe of the plurality of capture probes comprising a spatial barcode and a capture domain, wherein the second area is adjacent to the biological sample disposed on the array, wherein the capture domain of the capture probe of the first area of the array binds to the target nucleic acid; (b) extending a ligation product into the 5′ end of the capture probe of the first area of the array using the capture probe as a template; and (c) contacting the second area of the array with a solution comprising terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that one or more dideoxynucleotides are added to the capture domain of the capture probes.

Embodiment 30 is the method of embodiment 29, wherein the method further comprises removing the residual solution from the array.

Embodiment 31 is the method of embodiment 30, wherein the removing step comprises the use of a wash buffer comprising one or more of: a solvent, an acid, a base, and a buffer.

Embodiment 32 is the method of embodiment 31, wherein the wash buffer comprises phosphate buffered saline or saline sodium citrate.

Embodiment 33 is the method of any one of embodiments 23-32, wherein the biological sample is fixed and/or stained prior to step (a).

Embodiment 34 is the method of any one of embodiments 23-33, wherein the method further comprises, between steps (a) and (b), fixing and/or staining the biological sample.

Embodiment 35 is the method of embodiment 33 or embodiment 34, wherein the step of fixing the biological sample comprises the use of a fixative selected from the group consisting of ethanol, methanol, acetone, formaldehyde, paraformaldehyde-Triton, glutaraldehyde, and combinations thereof.

Embodiment 36 is the method of embodiment 35, wherein the step of staining the biological sample comprises the use of eosin and hematoxylin.

Embodiment 37 is the method of any one of embodiments 33-35, wherein the step of staining the biological sample comprises the use of a detectable label selected from the group consisting of a radioisotope, a fluorophore, a chemiluminescent compound, a bioluminescent compound, or a combination thereof.

Embodiment 38 is the method of any one of embodiments 1-37, wherein the dideoxynucleotide is ddATP or ddTTP.

Embodiment 39 is the method of any one of embodiments 1-38, wherein the solution comprises about 0.5 mM to about 25 mM of the dideoxynucleotide.

Embodiment 40 is the method of embodiment 39, wherein the solution comprises about 0.5 mM to about 1.5 mM of the dideoxynucleotide.

Embodiment 41 is the method of embodiment 40, wherein the solution comprises about 1 mM of the dideoxynucleotide.

Embodiment 42 is the method of any one of embodiments 1-41, wherein the solution further comprises CoCl₂.

Embodiment 43 is the method of embodiment 42, wherein the solution comprises about 0.1 mM to about 2 mM CoCl₂.

Embodiment 44 is the method of embodiment 42 or embodiment 43, wherein the solution comprises about 0.25 mM CoCl₂.

Embodiment 45 is the method of any one of embodiments 1-44, wherein the solution further comprises a buffer.

Embodiment 46 is the method of any one of embodiments 1-45, wherein the contacting step is performed for about 5 minutes to about 90 minutes.

Embodiment 47 is the method of embodiment 46, wherein the contacting step is performed for about 60 minutes.

Embodiment 48 is the method of any one of embodiments 1-47, wherein the contacting step is performed at a temperature of about 25° C. to about 45° C.

Embodiment 49 is the method of embodiment 48, wherein the contacting step is performed at a temperature of about 37° C.

Embodiment 50 is the method of any one of embodiments 1-49, wherein the removing step comprises the use of a wash buffer comprising one or more of: a solvent, an acid, a base, and a buffer.

Embodiment 51 is the method of embodiment 50, wherein the wash buffer comprises phosphate buffered saline or saline sodium citrate.

Embodiment 52 is a kit comprising: (a) a solution comprising terminal deoxynucleotidyl transferase; (b) one or more dideoxynucleotides; (c) a substrate comprising a plurality of capture probes, wherein the capture probes comprises a spatial barcode and a capture domain; and (d) instructions for performing the method of any one of embodiments 1-51.

Embodiment 53 is the kit of embodiment 52, wherein the kit further comprises a fixative selected from the group consisting of ethanol, methanol, acetone, formaldehyde, paraformaldehyde-Triton, glutaraldehyde, and combinations thereof.

Embodiment 54 is the kit of embodiment 52 or embodiment 53, wherein the dideoxynucleotide is ddATP or ddTTP.

Embodiment 55 is the kit of any one of embodiments 52-54, wherein the solution comprises about 0.5 mM to about 25 mM of the dideoxynucleotide.

Embodiment 56 is the kit of embodiment 55, wherein the solution comprises about 0.5 mM to about 1.5 mM of the dideoxynucleotide.

Embodiment 57 is the kit of embodiment 56, wherein the solution comprises about 1 mM of the dideoxynucleotide.

Embodiment 58 is the kit of any one of embodiments 52-57, wherein the solution further comprises CoCl₂.

Embodiment 59 is the kit of embodiment 58, wherein the solution comprises about 0.1 mM to about 2 mM CoCl₂.

Embodiment 60 is the kit of embodiment 58 or 59, wherein the solution comprises about 0.25 mM CoCl₂.

Embodiment 61 is the kit of any one of embodiments 52-60, wherein the solution further comprises a buffer.

Embodiment 62 is the kit of any one of embodiments 52-61, wherein the kit further comprises a wash buffer comprising one or more of: a solvent, an acid, a base, and a buffer.

Embodiment 63 is the kit of embodiment 62, wherein the wash buffer comprises phosphate buffered saline.

Embodiment 64 is the kit of embodiment 62, wherein the wash buffer comprises saline sodium citrate. 

What is claimed is:
 1. A method for determining a location of a target nucleic acid in a biological sample, the method comprising: (a) disposing the biological sample onto an array at a first area, wherein the array comprises a plurality of capture probes, wherein: a first capture probe of the plurality of capture probes comprises a first spatial barcode and a capture domain, wherein the first capture probe is comprised in the first area of the array; and a second area of the array comprises a second capture probe of the plurality of capture probes, wherein the second capture probe comprises a second spatial barcode and the capture domain, wherein the second area is not covered by the biological sample disposed on the array; (b) contacting the second area of the array with a solution comprising terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that a dideoxynucleotide is incorporated into the capture domain of the second capture probe; (c) permeabilizing the biological sample, such that the capture domain of the first capture probe hybridizes to the target nucleic acid from the biological sample; and (d) determining (i) a sequence of the first spatial barcode of the first capture probe, or a complement thereof, and (ii) all or a portion of a sequence of the target nucleic acid, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.
 2. The method of claim 1, further comprising removing residual solution from the second area of the array, wherein the removing comprises use of a wash buffer comprising one or more of: a solvent, an acid, a base, and a buffer.
 3. The method of claim 2, wherein the removing residual solution from the second area of the array occurs prior to permeabilizing in step (c).
 4. The method of claim 1, further comprising extending a 3′ end of the first capture probe of the first area of the array using the target nucleic acid as a template, thereby generating an extended capture probe.
 5. The method of claim 1, wherein the determining in step (d) comprises sequencing (i) the spatial barcode of the first capture probe, or a complement thereof, and (ii) all or a portion of the target nucleic acid, or a complement thereof.
 6. The method of claim 1, wherein the permeabilizing comprises use of a permeabilization agent selected from the group consisting of: an endopeptidase, a protease, sodium dodecyl sulfate, polyethylene glycol tert-octylphenyl ether, polysorbate 80, polysorbate 20, N-lauroylsarcosine sodium salt solution, saponin, and t-octylphenoxypolyethoxyethanol.
 7. The method of claim 1, further comprising fixing, staining, and/or imaging the biological sample.
 8. The method of claim 7, wherein staining the biological sample comprises use of eosin and/or hematoxylin; or use of a detectable label selected from the group consisting of a radioisotope, a fluorophore, a chemiluminescent compound, a bioluminescent compound, and a combination thereof.
 9. The method of claim 7, wherein the biological sample is fixed with a fixative selected from the group consisting of: ethanol, methanol, acetone, formaldehyde, paraformaldehyde-t-octylphenoxypolyethoxyethanol, glutaraldehyde, and combinations thereof.
 10. The method of claim 1, wherein the dideoxynucleotide is ddATP or ddTTP.
 11. The method of claim 1, wherein the solution comprises about 0.5 mM of the one or more dideoxynucleotides to about 25 mM of the one or more dideoxynucleotides.
 12. The method of claim 1, wherein the solution comprises about 0.1 mM CoCl₂ to about 2 mM CoCl₂.
 13. The method of claim 1, wherein the contacting step is performed for about 5 minutes to about 90 minutes and at a temperature of about 25° C. to about 45° C.
 14. The method of claim 1, wherein the biological sample is a tissue section.
 15. The method of claim 4, wherein the method further comprises generating a nucleic acid molecule complementary to the extended capture probe.
 16. A method for determining a location of a target nucleic acid in a biological sample, the method comprising: (a) disposing the biological sample onto an array at a first area, wherein the array comprises a plurality of capture probes, wherein: a first capture probe of the plurality of capture probes comprises a first spatial barcode and a capture domain, wherein the first capture probe is comprised in the first area of the array; and a second area of the array comprises a second capture probe of the plurality of capture probes, wherein the second capture probe comprises a second spatial barcode and the capture domain, wherein the second area is not covered by the biological sample disposed on the array, wherein the capture domain of the first capture probe hybridizes to a ligation product; (b) contacting the second area of the array with a solution comprising terminal deoxynucleotidyl transferase and one or more dideoxynucleotides, such that a dideoxynucleotide is incorporated into the capture domain of the second capture probe; (c) permeabilizing the biological sample; (d) extending the ligation product toward the 5′ end of the first capture probe using the first capture probe as a template; and (e) determining (i) a sequence of the first spatial barcode of the first capture probe, or a complement thereof, and (ii) all or a portion of a sequence of the ligation product, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.
 17. The method of claim 16, further comprising removing residual solution from the second area of the array, wherein the removing comprises use of a wash buffer comprising one or more of: a solvent, an acid, a base, and a buffer.
 18. The method of claim 17, wherein the removing residual solution from the second area of the array occurs prior to the permeabilizing in step (c).
 19. The method of claim 16, wherein the extending in step (d) further comprises extending a 3′ end of the first capture probe using the ligation product as a template, thereby generating an extended capture probe.
 20. The method of claim 16, wherein the determining in step (e) comprises sequencing (i) the first spatial barcode of the first capture probe, or a complement thereof, and (ii) all or a portion of the ligation product, or a complement thereof.
 21. The method of claim 16, further comprising fixing, staining, and/or imaging the biological sample.
 22. The method of claim 21, wherein the biological sample is fixed with a fixative selected from the group consisting of ethanol, methanol, acetone, formaldehyde, paraformaldehyde-t-octylphenoxypolyethoxyethanol, glutaraldehyde, and combinations thereof.
 23. The method of claim 21, wherein staining the biological sample comprises use of eosin and/or hematoxylin; or use of a detectable label selected from the group consisting of a radioisotope, a fluorophore, a chemiluminescent compound, a bioluminescent compound, and a combination thereof.
 24. The method of claim 16, wherein the ligation product is generated by hybridizing a first probe and a second probe to the target nucleic acid, wherein the first probe and the second probe are ligated to form the ligation product.
 25. The method of claim 24, wherein the first probe or the second probe comprises an analyte capture sequence that hybridizes to the capture domain of the first capture probe.
 26. The method of claim 16, wherein the dideoxynucleotide is ddATP or ddTTP.
 27. The method of claim 16, wherein the solution comprises about 0.5 mM of the one or more dideoxynucleotides to about 25 mM of the one or more dideoxynucleotides.
 28. The method of claim 16, wherein the solution further comprises about 0.1 mM CoCl₂ to about 2 mM CoCl₂.
 29. The method of claim 16, wherein the contacting step is performed for about 5 minutes to about 90 minutes and at a temperature of about 25° C. to about 45° C.
 30. The method of claim 16, wherein the biological sample is a tissue section. 